weightmaxentropy: Search for the weights of the nests which maximize the...

In embryogrowth: Tools to Analyze the Thermal Reaction Norm of Embryo Growth

Search for the weights of the nests which maximize the entropy of nest temperatures distribution

Description

Search for the weights of the nests which maximize the entropy of nest temperatures distribution. Entropy is measured by Shanon index.
Entropy method must be entropy.empirical because it is the only method insensitive to scaling.
If no weight is given, the initial weight is uniformly distributed.
Use control_optim=list(trace=0) for not show progress of search report.

Usage

weightmaxentropy(
  temperatures = stop("Temperature data must be provided !"),
  weight = NULL,
  entropy.method = entropy::entropy.empirical,
  plot = TRUE,
  control_optim = list(trace = 0, maxit = 500),
  control_plot = NULL,
  control_entropy = NULL,
  col = c("black", "red")
)

Arguments

temperatures	Timeseries of temperatures formated using FormatNests()
weight	A named vector of the initial weight search for each nest for likelihood estimation
entropy.method	Entropy function, for example entropy::entropy.empirical. See package entropy for description
plot	Do the plot of temperatures before and after weight must be shown ? TRUE or FALSE
control_optim	A list with control paramaters for optim function
control_plot	A list with control paramaters for plot function
control_entropy	A list with control paramaters for entropy function
col	Colors for unweighted and weighted distributions

Details

Search for the weights of the nests which maximize the entropy of nest temperatures distribution

Value

A named vector of weights

Author(s)

Marc Girondot

Examples

## Not run: 
library(embryogrowth)
data(nest)
formated <- FormatNests(nest)
w <- weightmaxentropy(formated, control_plot=list(xlim=c(20,36)))
x <- structure(c(120.940334922916, 467.467455887442,  
	306.176613681557, 117.857995419495),  
	.Names = c("DHA", "DHH", "T12H", "Rho25"))
# pfixed <- c(K=82.33) or rK=82.33/39.33
pfixed <- c(rK=2.093313)
# K or rK are not used for dydt.linear or dydt.exponential
resultNest_4p_weight <- searchR(parameters=x,  
	fixed.parameters=pfixed, temperatures=formated,  
	integral=integral.Gompertz, M0=1.7, hatchling.metric=c(Mean=39.33, SD=1.92),  
	method = "BFGS", weight=w)
data(resultNest_4p_weight)
plotR(resultNest_4p_weight, ylim=c(0,0.50), xlim=c(15, 35))
# Standard error of parameters can use the GRTRN_MHmcmc() function

## End(Not run)

embryogrowth documentation built on Sept. 11, 2024, 8:16 p.m.